These observations, in agreement with studies that have addressed this question directly (Kuczynski et al., 2010), suggest that increasing the sequencing depth is not likely to provide additional insight into questions of beta diversity, and we therefore argue that (for questions of beta diversity in particular) the decreased cost of sequencing should be applied to study microbial systems using many more samples, for example, in dense temporal or spatial analyses, rather than with many more sequences per sample. Of course, if the objective is to identify taxa that are very rare in communities, deeper sequencing will be advantageous. Additionally we note that while as few as 10 sequences per sample may be useful for differentiating very different environment types (for example, soil and feces), as environments become more similar (for example, two soil samples of different pH) more sequences will be required to differentiate them.

Anyway the article describes the "Micro'be'" project for which more details are available here. Some interesting details at that site include a description

Imagine a fabric that grows...a garment that forms itself without a single stitch!
The fashion that starts with a bottle of wine...
Micro'be' fermented fashion investigates the practical and cultural biosynthesis of clothing - to explore the possible forms and cultural implications of futuristic dress-making and textile technologies.
Instead of lifeless weaving machines producing the textile, living microbes will ferment a garment.
A fermented garment will not only rupture the meaning of traditional interactions with body and clothing; but also raise questions around the contentious nature of the living materials themselves.
This project redefines the production of woven materials.
By combining art and science knowledge and with a little inventiveness, the ultimate goal will be to produce a bacterial fermented seamless garment that forms without a single stitch.

So - in essence they are trying to grow clothing as a side product of wine fermentation. Not sure what it is like to wear such clothing - or to be around someone wearing it - but it is a fun idea.

The archaea reference was in a quote that this article made of a Science Daily report

"The microbes in the human gut belong to three broad domains, defined by their molecular phylogeny: Eukarya, Bacteria, and Achaea."

Wow - this surprised me. An article at some place called Food Consumer that was mentioning archaea.

But that was pretty much the only decent part. Things went downhill fast with a link to some total BS on a way to cure every disorder on the planet by focusing on gut microbial health.

The article then pulls a classic trick - referencing some of the new human micro biome work in Nature to make the discussion here seem scientific. But alas it is not. Consider this doozy of a line

"The ideal balance of beneficial to pathogenic bacteria in your gut is about 85 percent good bacteria and 15 percent bad. Maintaining this ideal ratio is what it's all about when we're talking about optimizing your gut health. "

Yes that is right everyone - you want to maintain a ratio where 15% of the bacteria in your gut are pathogenic. Aaarrggh.

Not surprisingly, when I searched around the web for detail on the person behind this article - some Dr. Mercola - who I have never heard of - I discovered that he is considered by many to be a quack. No disagreement from me.

Wednesday, June 27, 2012

Just got back from the Canadian Society for Microbiology meeting where I gave the keynote talk on the last day of the meeting (Saturday). Was a very short, but good trip. Got to see some key collaborators and colleagues and Vancouver was very nice for the few days I was there.

I recorded my talk on my laptop using the Keynote "Record Slideshow" function. I then exported it to Slideshare (just the slides - no audio) and to Youtube (video of slides with audio). They are posted below. I also did a mini storification of my talk which is also below.

Friday, June 22, 2012

Well without a doubt the biggest surprise to me of the American Society for Microbiology General Meeting was the massive increase in the use of Twitter compared to previous years. Microbiologist are clearly just way way ahead of the curve compared to other scientists on this. The tweets and retweets and discussion of tweets was so extensive that #ASM2012 was a trending topic on twitter for much of the time during the meeting:

For those not familiar with Twitter - this abbreviation w/ the # is known as a hashtag - and if everyone at a meeting uses this hashtag in their posts about the meeting then it is easy to keep track of all the meeting posts by searching for posts with that hashtag. Such searches can be done in real time with various Twitter clients or via the Twitter website.

Saturday, June 16, 2012

Making a list of blogs that focus entirely or partly on microbiology topics. Here are some. Would love suggestions for others. Obviously not all are of equal quality in terms of the writing or the science but the diversity is impressive.

Friday, June 15, 2012

The American Society for Microbiology meeting is starting tomorrow and there are multiple things related to microbiology of the built environment there. These include a session that was organized by Brendan Bohannan which I am chairing.

The details of the session are below:

Session Title: The Great Indoors: Recent Advances in the Ecology of Built Environments

Session Date/Time: Sunday Jun 17, 2012 3:00 PM - 5:30 PM

Session Room: Esplanade Ballroom 300

Description:
Although humans in industrialized countries spend nearly 90% of their time in enclosed buildings, we know very little about the biology of the indoor environment. However, this is starting to change. Over the past few years, the field of indoor ecology has grown dramatically. Ecologists are beginning to apply ecological theory and concepts to understanding buildings as ecosystems. A new understanding of the biodiversity of built environments is emerging, as well as a new appreciation of the importance of interactions between humans and non-human life indoors. The proposed symposium will showcase this emerging understanding. We will feature presentations that demonstrate the utility of ecological theory for understanding built environments, that describe the dynamics of biodiversity indoors and that illustrate the interactions of humans with indoor ecology. Our focus will be on the ecology of the dominant forms of non-human life indoors - microorganisms - and their interactions with humans.

Monday, June 11, 2012

A few days ago I wrote a post:Report on "Egregious Academic Freedom Violation" at #UCDavis. The post provides some detail on an investigation carried out by the UC Davis Academic Senate into a case of apparent retribution at the UC Davis medical school. In the case the Dean of the Medical School (Claire Pomeroy), the Executive Associate Dean Fred Meyers and the Health System Counsel appear to have carried out a retribution of sorts against a member of the faculty at the medical school (NOTE - I have a half appointment at the medical school). The faculty member - Michael Wilkes had the gall to write an editorial (with Jerome Hoffman) for the SF Chronicle expressing opinions about a medical issue and actions of some people at the UC Davis Medical School. Apparently, some people at the medical school did not like being criticized. The result? A threat to take away his space, to remove him as instructor of a medical school course, and other incites including a threatening email/letter from the medical school counsel. Lovely.

Fortunately, the UC Davis Academic Senate was brought into the case by Wilkes and a committee of the academic senate responded VERY strongly with a report (see my previous post with more detail). Meanwhile - news of the report spread and was covered in Inside Higher Ed. It was then that I heard about it and felt the need to blog about it. And news has spread a bit more (thank you PZ Myers and others). On Friday, the UC Davis Academic Senate met (and though I am not a member of the Senate, I went to the meeting). And the Senate passed three resolutions coming out strongly in support of Prof. Wilkes and critiquing the behavior of the Dean, Asst. Dean and Counsel from the Med. School. Just after the resolution was passed the faculty received an email from the Provost Ralph Hexter that was very strongly saying he supported academic freedom on campus.

So that is where we stand now. I am very pleased with the Provost's statement. At the same time I am still dismayed at the reported behavior of the Medical School administration. And I think this issue needs to still get some air until there are repercussions for the Medical School actions ...

Here are some related links and updates that I collected as the story has unfolded.

Friday, June 08, 2012

The following statement was issued today by UC Davis Provost and Executive Vice Chancellor Ralph Hexter:

In March, 1953 the Association of American Universities (AAU) adopted a statement articulating "The Rights and Responsibilities of Universities and Their Faculties." It includes these words:

"A university must…be hospitable to an infinite variety of skills and viewpoints, relying upon open competition among them as the surest safeguard of truth. Its whole spirit requires investigation, criticism, and presentation of ideas in an atmosphere of freedom and mutual confidence. This is the real meaning of 'academic' freedom."

A committee of our campus's Academic Senate has devoted considerable time and effort to examining an assertion by a faculty member of the UC Davis School of Medicine that his academic freedoms were compromised by school administrators. Our Senate's Representative Assembly earlier today heard and ratified the committee's findings.

Academic freedom is sacrosanct at UC Davis, and the underlying assertions in this matter are deeply troubling. My office will review this case and take appropriate actions.

Wednesday, June 06, 2012

Crossposting this here --- posted originally on my lab blog. NOTE - many updates down below at the bottom of page.

Wow -- just got this email regarding Academic Senate issues at UC Davis and found out about this report on “Egregious Academic Freedom Violation” in relation to an issue at the Medical School. See email below as well as the report (see link) - starting on p62. It is a pretty sordid tale ... (with some highlighting now added by me)

The email I received:

*Sent on behalf of the Academic Senate Chair*

Dear Academic Senate Members,

On Friday, the Academic Senate Committee on Academic Freedom and Responsibility (CAFR) will be presenting their report, “Egregious Academic Freedom Violation” which begins on page 62 of the June 8 Representative Assembly meeting call (http://academicsenate.ucdavis.edu/ra/RA-Meeting-Call-2012-06-08.pdf). The Committee on Elections, Rules and Jurisdiction (CERJ) has put the recommendations of the CAFR report into the form of resolutions, which are attached. In order to be voted on by the Representative Assembly, the resolutions would have to be moved and seconded. We hope that the attachment will assist the Representative Assembly as its members review and consider CAFR’s recommendations.

Tuesday, June 05, 2012

As many may know - I am pretty obsessed with the uses of phylogeny in biological studies. In fact, one could say this has driven almost all of my work. Thus when an email went around a little bit ago about an article for a journal club at UC Davis where the title begins with "Does phylogeny matter?", well, I had to take a look. Alas, I was a bit worried when I saw the article was in Ecology Letters because I am at home and was not sure about access policies for this journal.

And I was even more pleasantly surprised to look over the article. Many meta-analyses can seem forced - if not almost unbearable to look through. But this one is very well done. Basically they did a massive comparison of conclusions that one could reach when one either does or does not take into account the phylogenetic non-independence of taxa when conducting meta-analyses in evo-eco studies. They searched published literature for meta-analyses and then .. well I will use their words here (from the end of their introduction):

Monday, June 04, 2012

OK. I love that people ask me lots of questions about evolution, genomics, microbes, a mix of the two, etc. But I just cannot keep answering single one-off emails about these topics. So I am starting online office hours. If you have any general questions about phylogenetics, evolution, genomics, microbes, or any of the work done in my lab, please post your questions here. And I will try to answer them.

So I decided to check it out. The piece is titled It's Time to Bet on Genomics and it is, well, just completely in appropriate. Sure - it does take on an article that itself was over the top in downplaying the power of genomics (see Erika Check Hayden's article about that issue here). But then Davis goes on to write about a company founded by an ex post doc of his for which Davis is one of the advisors (he does kindly let us know this, but still ...). And what he writes he is a big big pile of fluff with no evidence presented. Among the lines in the "essay" I find disturbing:

One of the most interesting of these is being developed by Genophen

Genophen’s application is rather breathtaking in its ambition.

Genophen’s “risk engine”—a simple term for some very complex data mining and computer modeling—will map your risk factors against the world’s vast library of medical research and then offer up a personalized set of behavior and treatment recommendations that can help you reduce those risks . . . and even prevent disease itself.

We are now at the point where genomics-enabled medical technology can run various what-if scenarios and show you whether diet, exercise, medication, or some other factor or combination of factors has the greatest statistical likelihood of reducing that risk. The information can then be visually displayed through charts and graphs and made available to patients and their doctors via secure web-based portals.

But instinctively I believe it to be true, and anecdotally Genophen’s first trial provided some confirmation.

All of this without any link to a paper, without any data, without any real details. Shameful. Not saying genomic medicine does not have a lot of promise. But this "essay" is so excessively focused on PR for one company that there is no reason to have any faith in anything said in it. I am therefore giving Ron Davis and Forbes my coveted Overselling Genomics Award (#7). Plus I think Forbes deserves some sort of award for "Publishing PR" but I will have to think one of those up. This piece almost certainly never should have been published at Forbes.Com without many many more caveats. Yuck.

UPDATE - here is a screenshot from the Forbes Web site. It is marked as "Forbes Leadership Forum" ... hard to tell whether it is meant as an essay, editorial, op-ed, or what.

Saturday, June 02, 2012

Just got back from a Sloan Foundation funded meeting in Boulder, Colorado that focused on microbiology of the built environment. More on that another time. What I want to tell you about - no - what I need to tell you about - is the entertainment that the meeting organizers arranged at dinner Thursday night.

We had dinner at Red Lion Restaurant - a phenomenally gorgeous spot in the canyon just West of Boulder. And while we were milling around before dinner I saw out of the corner of my eye a woman walking in to the tent where we were to have dinner. She was dressed in almost all white and was carrying a giant silver spoon. So I asked the meeting organizer - Mark Hernandez - if she was the entertainment. And surprisingly he said - yes - she was a dancer and Professor at Boulder and also did a kind of science performance art.

Her name was Michelle Ellsworth and he said she was amazing. So I was very intrigued as I am a big fan of mixing science and art. So I went over to where she had set up and asked her a few questions and took her picture ...

I grabbed a seat near the front of the area they set up for her. And Mark Hernandez introduced her

And then I witnessed what I consider to be - seriously - the most entertaining presentation I have ever seen at a conference. She presented her "Preparation Y" project focused on what should be done to prepare for "the obsolescence of the Y chromosome." She then proceeded to discuss some relatively recent work on Y chromosome evolution in humans as well as an article about this by Maureen Dowd. And she posed the questions (tongue planted firmly in cheek ... though done in a style that was remarkably earnest ...)